I constantly use the brightness, mission control, volume, and iTunes playback shortcuts on my keyboard's function row. However, a handful of apps I use make heavy use of F1, F2, etc. for keyboard shortcuts, and it's annoying having to use something like Fn+F7 all the time for something that was intended to be a single keystroke away.

I can think of a few ways to get around this problem:

Manually reassign any and all keyboard shortcuts that make use of function keys to something else. Ugh.

Enable the "Use all F1, F2, etc. keys as standard function keys" option in System Preferences, and re-train myself to use Fn whenever I want to use the system shortcuts. Ugh.

Find a way to enable this option only for certain applications.

Is this possible to do? Are there any third-party apps that can take care of this for me?

I've seen this application before when I was just browsing, never used it though. It's called FunctionFlip.

FunctionFlip individually controls your MacBook or MacBook Pro's function keys, turning special keys back to regular F-keys, or vice-versa. FunctionFlip is a preference pane; you'll find it in the "Other" category in System Preferences.